EMPeror 1.0.0-beta.20 – Analysis of High Throughput Microbial Ecology datasets

EMPeror 1.0.0-beta.20

:: DESCRIPTION

Emperor is an interactive next generation tool for the analysis, visualization and understanding of high throughput microbial ecology datasets.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

 EMPeror

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python
  • Numpy
  • qcli

:: DOWNLOAD

 EMPeror

 :: MORE INFORMATION

Citation

EMPeror: a tool for visualizing high-throughput microbial community data.
Vázquez-Baeza Y, Pirrung M, Gonzalez A, Knight R.
Gigascience. 2013 Nov 26;2(1):16. doi: 10.1186/2047-217X-2-16.

E-vident – Elucidating Sampling Effort for Microbial Analysis Studies

E-vident

:: DESCRIPTION

Evident is a web-based software tool with an interactive user interface, implemented in HTML, Web Graphics Library, mod_python and QIIME. The interface of E-vident (Fig. 1) is comprised of: (i) the selection of parameters (i.e., study of interest, number of sequences per sample, the number of samples to use, and the number of iterations); (ii) the kind of visualizations to generate (Demo PCoA shows the original results from the study, and PCoA recalculates the study using the user-defined parameters in (i); (iii) the WebGL plot display.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

Evident

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Apache
  • QIIME
  • Python

:: DOWNLOAD

 E-vident

:: MORE INFORMATION

RevEcoR 0.99.3 / shiny-RevEcoR 0.1.1 – Reverse Ecology Analysis of Microbiomes

RevEcoR 0.99.3 / shiny-RevEcoR 0.1.1

:: DESCRIPTION

RevEcoR is an R package that implements the reverse ecology algorithm for determining microbe-microbe interactions in microbial communities.

shiny-RevEcoR is an interactive web application that provides a flexible graphical user interface (GUI) to the Reverse Ecology analysis package for R, called RevEcoR hosted on CRAN.

::DEVELOPER

Yang Cao <yiluheihei at gmail.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 RevEcoR , shiny-RevEcoR

:: MORE INFORMATION

Citation

RevEcoR: an R package for the reverse ecology analysis of microbiomes.
Cao Y, Wang Y, Zheng X, Li F, Bo X.
BMC Bioinformatics. 2016 Jul 29;17(1):294. doi: 10.1186/s12859-016-1088-4.

NetCooperate – Determining Host-microbe and Microbe-microbe Cooperation

NetCooperate

:: DESCRIPTION

NetCooperate is a web tool and a software package for determining host-microbe and microbe-microbe cooperative potential.

::DEVELOPER

the Borenstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 NetCooperate

:: MORE INFORMATION

Citation

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation.
Levy R, Carr R, Kreimer A, Freilich S, Borenstein E.
BMC Bioinformatics. 2015 May 17;16:164. doi: 10.1186/s12859-015-0588-y.

mcaGUI 1.16.0 – Microbial Community Analysis Graphical User Interface

mcaGUI 1.16.0

:: DESCRIPTION

mcaGUI is a microbial community analysis GUI for R using gWidgets.

::DEVELOPER

Wade K. Copeland

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 mcaGUI

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Aug 15;28(16):2198-9. doi: 10.1093/bioinformatics/bts338. Epub 2012 Jun 12.
mcaGUI: microbial community analysis R-Graphical User Interface (GUI).
Copeland WK1, Krishnan V, Beck D, Settles M, Foster JA, Cho KC, Day M, Hickey R, Schütte UM, Zhou X, Williams CJ, Forney LJ, Abdo Z.

SRA 2.0b – Single Strain Regression Analysis

SRA 2.0b

:: DESCRIPTION

SRA is a methodological innovation for calibration of the disk diffusion antibiotic susceptibility test.It is also a method suitable for analysis of different disk potencies of new antibiotics.

::DEVELOPER

G.Kronvall @ Christian Giske Group

:: SCREENSHOTS

SRA

:: REQUIREMENTS

  • Windows 

:: DOWNLOAD

 SRA

:: MORE INFORMATION

Citation

Scand J Infect Dis. 2000;32(6):633-6.
Fusidic acid disk diffusion testing of clostridium difficile can be calibrated using single-strain regression analysis.
Oppenheimer M, Kronvall G, Karlsson I, Holst E.

GrowthRates 1.9 – Calculates Bacterial Growth Rates

GrowthRates 1.9

:: DESCRIPTION

GrowthRates is a program that calculates bacterial growth rates from the data generated by a micro-plate reader used to monitor the growth of bacterial cultures in micro-plate wells. The program automatically identifies the exponential phase of the growth curve and uses that portion of the curve to calculate growth rates and std. errors of those rates

::DEVELOPER

Bellingham Research Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 GrowthRates

:: MORE INFORMATION

MycPermCheck 1.1 – Mycobacterium Tuberculosis Permeability Prediction tool for small Molecules

MycPermCheck 1.1

:: DESCRIPTION

MycPermCheck, given the current lack of precise molecular criteria determining mycobacterial permeability, represents an unprecedented prediction tool intended to support antimycobacterial drug discovery.

::DEVELOPER

the Research Group of Prof. Sotriffer

 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Merget et al. (2013)
MycPermCheck: The Mycobacterium tuberculosis permeability prediction tool for small molecules,
Bioinformatics, 29(1): 62-68.

micropower – Power Estimation for Microbiome Studies

micropower

:: DESCRIPTION

The micropower package is designed to facilitate power estimation for microbiome studies that will be analyzed with pairwise distances (beta diversity) and PERMANOVA (a non-parametric extension of multivariate analysis of variance to a matrix of pairwise distances).

::DEVELOPER

Bushman Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 micropower

:: MORE INFORMATION

Citation

Power and Sample-Size Estimation for Microbiome Studies Using Pairwise Distances and PERMANOVA.
Kelly BJ, Gross R, Bittinger K, Sherrill-Mix S, Lewis JD, Collman RG, Bushman FD, Li H.
Bioinformatics. 2015 Mar 29. pii: btv183.